Technical Abstract:
In this paper we describe the development and characterization of the first high density SNP chip for rainbow trout. The chip included 57,500 putative SNPs, of which 49,500 (86%) were validated as high quality and polymorphic in our validation panel of 960 rainbow trout samples. This array is comparable to those of other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. The SNPs are distributed throughout the genome with good representation across all 29 chromosomes. The chip is more useful for rainbow trout aquaculture populations with more than 83% polymorphic markers per population, however in wild populations the number of polymorphic markers was greater than 10,000. The SNP chip is publicly available and it has already been used in a proof- of concept study to demonstrate its utility for genome enabled selection in rainbow trout presented in a companion WCGALP 2014 paper by Vallejo et al.